BaseSpaceR Adrian Alexa [email protected]. BaseSpace - Plug and Play Genomic Cloud Solution From Sample to Biological Insight. Seamless Instrument Integration Harness the Internet Accessible to Everyone. Data transferred as the instrument runs - PowerPoint PPT Presentation
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1) Authentication [3 lines of code]– User needs to interact with the BaseSpace UI (or via a web server).
2) Select a sample (collection of FASTQ files) from the Project of your choice [3 lines]
3) Download the files (FASTQs in our case) [4 lines]
4) Process the downloaded files and compute the stats […]5) Upload results back to BaseSpace [~10 lines]
– Results are collection of files for now, minimal visualisation.
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Amplification of distal chr8q.
Homozygous deletion of part of chr8p.
Location of centromeres indicated by vertical dotted lines
Detect amplifications and deletions in cancer samples
Data can be obtained from a single MiSeq runs (one for tumor and one for normal or even both on a flowcel).
Typical analysis requires only the coverage data and this can be directly obtained using a REST method.
Corrects for tumor ploidy and purity.
Copy Number AbnormalitiesAccessing the coverage via a high-level REST method
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RConsoleExploring BaseSpace data using RStudio
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What’s next
Facilitate the use of Bioconductor packages – there is much to gain if as many Bioconductor packages as possible can consume data (directly) from BaseSpace.
Introduce high-level methods (REST or R API) for random access to BAMs, VCFs, metric data, etc. One can already use Rsamtools for indexed BAMs.
R level methods to facilitate RNAseq, ChipSeq, etc. analyses.
BaseSpace Data Central – publicly available data – most of it will be data coming from our latest instruments, chemistry, workflows.
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Resources
Tutorials, videos, whitepapers and other educational material:http://www.illumina.com/software/basespace/basespace-education.ilmn